Proximity-CLIP provides a snapshot of protein-occupied RNA elements at subcellular resolution and transcriptome-wide scale

Daniel Benhalevy, Markus Hafner

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

Abstract

The distribution of messenger RNAs (mRNAs) to specific subcellular locations has been studied for the past two decades. Technically, studies of RNA localization are lagging those related to protein localization. Here we provide a detailed protocol for Proximity-CLIP, a method recently developed by our group, that combines proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced protein-RNA cross-linking to simultaneously profile the proteome including RNA-binding proteins (RBPs) and the RBP-bound transcriptome in any given subcellular compartment. The approach is fractionation independent and also enables studying localized RNA-processing intermediates, as well as the identification of regulatory cis-acting elements on RNAs occupied by proteins in a cellular compartment-specific manner.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages283-305
Number of pages23
DOIs
StatePublished - 2020
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume2166
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • RNA localization
  • RNA regulatory elements
  • RNA-processing intermediates
  • RNA-protein interactions
  • Subcellular RNA biology

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